
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:18 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4787.phylip" (19 taxa, 779 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
GTRI	44	-3982.4990	8058.3931	0.5087	0.5087
HKYI	40	-3987.5527	8059.5497	0.2853	0.7940
GTRIG	45	-3982.9743	8061.5965	0.1025	0.8965
HKYIG	41	-3988.0905	8062.8539	0.0547	0.9511
GTRG	44	-3985.3000	8063.9950	0.0309	0.9820
HKYG	40	-3990.3194	8065.0832	0.0179	1.0000
K2PI	37	-4001.4329	8080.6607	0.0000	1.0000
K2PIG	38	-4000.9962	8081.9977	0.0000	1.0000
SYMI	41	-3998.5463	8083.7655	0.0000	1.0000
K2PG	37	-4003.0116	8083.8180	0.0000	1.0000
SYMIG	42	-3998.2531	8085.4139	0.0000	1.0000
SYMG	41	-4000.2509	8087.1748	0.0000	1.0000
GTR	43	-4062.1970	8215.5423	0.0000	1.0000
HKY	39	-4067.3167	8216.8554	0.0000	1.0000
K2P	36	-4081.3318	8238.2539	0.0000	1.0000
SYM	40	-4078.4771	8241.3986	0.0000	1.0000
F81IG	40	-4080.4263	8245.2970	0.0000	1.0000
F81G	39	-4082.7338	8247.6894	0.0000	1.0000
F81I	39	-4083.7314	8249.6847	0.0000	1.0000
JC69IG	37	-4091.0545	8259.9038	0.0000	1.0000
JC69G	36	-4094.3572	8264.3047	0.0000	1.0000
JC69I	36	-4094.5981	8264.7865	0.0000	1.0000
F81	38	-4158.4965	8396.9984	0.0000	1.0000
JC69	35	-4170.7871	8414.9659	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-3982.4990	8052.9980	0.5764	0.5764
HKYI	40	-3987.5527	8055.1053	0.2010	0.7773
GTRIG	45	-3982.9743	8055.9485	0.1318	0.9092
HKYIG	41	-3988.0905	8058.1809	0.0432	0.9523
GTRG	44	-3985.3000	8058.5999	0.0350	0.9874
HKYG	40	-3990.3194	8060.6387	0.0126	1.0000
K2PI	37	-4001.4329	8076.8659	0.0000	1.0000
K2PIG	38	-4000.9962	8077.9923	0.0000	1.0000
SYMI	41	-3998.5463	8079.0925	0.0000	1.0000
K2PG	37	-4003.0116	8080.0231	0.0000	1.0000
SYMIG	42	-3998.2531	8080.5063	0.0000	1.0000
SYMG	41	-4000.2509	8082.5018	0.0000	1.0000
GTR	43	-4062.1970	8210.3940	0.0000	1.0000
HKY	39	-4067.3167	8212.6335	0.0000	1.0000
K2P	36	-4081.3318	8234.6636	0.0000	1.0000
SYM	40	-4078.4771	8236.9542	0.0000	1.0000
F81IG	40	-4080.4263	8240.8526	0.0000	1.0000
F81G	39	-4082.7338	8243.4675	0.0000	1.0000
F81I	39	-4083.7314	8245.4627	0.0000	1.0000
JC69IG	37	-4091.0545	8256.1089	0.0000	1.0000
JC69G	36	-4094.3572	8260.7144	0.0000	1.0000
JC69I	36	-4094.5981	8261.1962	0.0000	1.0000
F81	38	-4158.4965	8392.9930	0.0000	1.0000
JC69	35	-4170.7871	8411.5743	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-3987.5527	8241.4257	0.9011	0.9011
HKYG	40	-3990.3194	8246.9592	0.0566	0.9577
HKYIG	41	-3988.0905	8249.1594	0.0189	0.9766
K2PI	37	-4001.4329	8249.2123	0.0184	0.9949
K2PG	37	-4003.0116	8252.3695	0.0038	0.9987
K2PIG	38	-4000.9962	8254.9968	0.0010	0.9997
GTRI	44	-3982.4990	8257.9505	0.0002	1.0000
GTRG	44	-3985.3000	8263.5524	0.0000	1.0000
GTRIG	45	-3982.9743	8265.5590	0.0000	1.0000
SYMI	41	-3998.5463	8270.0710	0.0000	1.0000
SYMG	41	-4000.2509	8273.4802	0.0000	1.0000
SYMIG	42	-3998.2531	8276.1427	0.0000	1.0000
HKY	39	-4067.3167	8394.2959	0.0000	1.0000
K2P	36	-4081.3318	8402.3520	0.0000	1.0000
GTR	43	-4062.1970	8410.6885	0.0000	1.0000
SYM	40	-4078.4771	8423.2746	0.0000	1.0000
F81G	39	-4082.7338	8425.1300	0.0000	1.0000
F81I	39	-4083.7314	8427.1252	0.0000	1.0000
F81IG	40	-4080.4263	8427.1730	0.0000	1.0000
JC69G	36	-4094.3572	8428.4028	0.0000	1.0000
JC69IG	37	-4091.0545	8428.4553	0.0000	1.0000
JC69I	36	-4094.5981	8428.8846	0.0000	1.0000
F81	38	-4158.4965	8569.9974	0.0000	1.0000
JC69	35	-4170.7871	8574.6046	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4787.phylip = 1 - 779;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4787.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4787.phylip = 1 - 779;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4787.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4787.phylip = 1 - 779;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4787.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

